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Tree Diversity Analysis. A Manual and Software

for Common Statistical Methods for Ecological
and Biodiversity Studies

Book January 2005

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Roeland Kindt and Richard Coe

The entire Tree Diversity Analysis manual can be freely downloaded from URL
http://www.worldagroforestry.org/output/tree-diversity-analysis

The accompanying BiodiversityR package can be downloaded from URL https://cran.r-

project.org/package=BiodiversityR and the vegan community ecology package can be downloaded
from URL https://cran.r-project.org/package=vegan

BiodiversityR windows installation guidelines in R 3.3.2 (December 2016)

1. Download R 3.3.2 from URL http://cran.r-project.org/bin/windows/base/
2. Install R 3.3.2 with default options, except for
2.1. Startup options
Do you want to customize the startup options?
Yes (customized startup)
2.2. Display Mode
Do you prefer the MDI or SDI interface?
SDI (separate windows)
3. Launch R
4. Copy following command in R
install.packages(pkgs=c("BiodiversityR", "vegan",
"Rcmdr", "MASS", "mgcv",
"cluster", "RODBC", "rpart", "effects", "multcomp",
"ellipse", "maptree", "sp", "splancs", "spatial",
"akima", "nnet", "dismo", "raster", "rgdal",
"bootstrap", "PresenceAbsence",
"maxlike", "gbm", "randomForest", "gam", "earth", "mda",
"kernlab", "e1071", "glmnet", "sem", "rgl", "relimp",
"lmtest", "leaps", "Hmisc", "colorspace", "aplpack",
"abind", "XLConnect", "car", "markdown", "knitr",
"bootstrap", "PresenceAbsence",
"geosphere", "maptools", "rgeos"),
dependencies=c("Depends", "Imports"))
# you may need to create a personal folder if program files are write-protected

5. Launch BiodiversityR
library(BiodiversityR)

6. Launch Graphical User Interface of BiodiversityR

BiodiversityRGUI()

A tutorial for ensemble suitability modelling (not described in this manual) is available from URL
http://dx.doi.org/10.13140/RG.2.1.1993.7684
Tree diversity
analysis
A manual and software for common statistical
methods for ecological and biodiversity studies

Roeland Kindt and Richard Coe

World Agroforestry Centre, Nairobi, Kenya
Suggested citation: Kindt R and Coe R. 2005. Tree diversity analysis. A manual and software for
common statistical methods for ecological and biodiversity studies. Nairobi: World Agroforestry
Centre (ICRAF).

Published by the World Agroforestry Centre

United Nations Avenue
PO Box 30677, GPO 00100
Nairobi, Kenya
Tel: +254(0)20 7224000, via USA +1 650 833 6645
Fax: +254(0)20 7224001, via USA +1 650 833 6646
Email: icraf@cgiar.org
Internet:www.worldagroforestry.org

World Agroforestry Centre 2005

ISBN: 92 9059 179 X

Design and Layout: K. Vanhoutte

Printed in Kenya

This publication may be quoted or reproduced without charge, provided the source is
acknowledged. Permission for resale or other commercial purposes may be granted under
select circumstances by the Head of the Training Unit of the World Agroforestry Centre.
Proceeds of the sale will be used for printing the next edition of this book.
Contents
Contents
Acknowledgements iv

Introduction v

Overview of methods described in this manual vi

Chapter 1 Sampling 1

Chapter 2 Data preparation 19

Chapter 3 Doing biodiversity analysis with Biodiversity.R 31

Chapter 4 Analysis of species richness 39

Chapter 5 Analysis of diversity 55

Chapter 6 Analysis of counts of trees 71

Chapter 7 Analysis of presence or absence of species 103

Chapter 8 Analysis of differences in species composition 123

Chapter 9 Analysis of ecological distance by clustering 139

Chapter 10 Analysis of ecological distance by ordination 153

 Acknowledgements
We warmly thank all that provided inputs that
lead to improvement of this manual. We especially
appreciate the comments received during training
sessions with draft versions of this manual and the
accompanying software in Kenya, Uganda and
Mali. We are equally grateful to the thoughtful
reviews by Dr Simoneta Negrete-Yankelevich
(Instituto de Ecologa, Mexico) and Dr Robert
Burn (Reading University, UK) of the draft version
of this manual, and to Hillary Kipruto for help in
editing of this manual.
We highly appreciate the support of the
Programme for Cooperation with International
Institutes (SII), Education and Development
Division of the Netherlands Ministry of Foreign
Affairs, and VVOB (The Flemish Association
for Development Cooperation and Technical
Assistance, Flanders, Belgium) for funding the
iv
development for this manual. We also thank
VVOB for seconding Roeland Kindt to the World
Agroforestry Centre (ICRAF).
This tree diversity analysis manual was inspired
by research, development and extension activities
that were initiated by ICRAF on tree and landscape
diversification. We want to acknowledge the
various donor agencies that have funded these
activities, especially VVOB, DFID, USAID and
EU.
We are grateful for the developers of the R
Software for providing a free and powerful
statistical package that allowed development
of Biodiversity.R. We also want to give special
thanks to Jari Oksanen for developing the vegan
package and John Fox for developing the Rcmdr
package, which are key packages that are used by
Biodiversity.R.

This manual was prepared during training events
held in East- and West-Africa on the analysis of tree
diversity data. These training events targeted data
analysis of tree diversity data that were collected by
scientists of the World Agroforestry Centre (ICRAF)
and collaborating institutions. Typically, data were
collected on the tree species composition of quadrats
or farms. At the same time, explanatory variables
such as land use and household characteristics were
collected. Various hypotheses on the influence
of explanatory variables on tree diversity can be
tested with such datasets. Although the manual
was developed during research on tree diversity
on farms in Africa, the statistical methods can be
used for a wider range of organisms, for different
hierarchical levels of biodiversity, and for a wider
range of environments.
These materials were compiled as a second-
generation development of the Biodiversity Analysis
Package, a CD-ROM compiled by Roeland Kindt
with resources and guidelines for the analysis of
ecological and biodiversity information. Whereas
the Biodiversity Analysis Package provided a range
of tools for different types of analysis, this manual
is accompanied by a new tool (Biodiversity.R)
that offers a single software environment for all
the analyses that are described in this manual.
This does not mean that Biodiversity.R is the
only recommended package for a particular type
of analysis, but it offers the advantage for training
purposes that users only need to be introduced to
one software package for statistically sound analysis
of biodiversity data.
Introduction
It is never possible to produce a guide to all
the methods that will be needed for analysis of
biodiversity data. Data analysis questions are
continually advancing, requiring ever changing
data collection and analysis methods. This
manual focuses on the analysis of species survey
data. We describe a number of methods that can
be used to analyse hypotheses that are frequently
important in biodiversity research. These are not
the only methods that can be used to analyse these
hypotheses, and other methods will be needed
when the focus of the biodiversity research is
different.
Effective data analysis requires imagination and
creativity. However, it also requires familiarity
with basic concepts, and an ability to use a set
of standard tools. This manual aims to provide
that. It also points the user to other resources that
develop ideas further.
Effective data analysis also requires a sound and
up to date understanding of the science behind
the investigation. Data analysis requires clear
objectives and hypotheses to investigate. These
have to be based on, and push forward, current
understanding. We have not attempted to link the
methods described here to the rapidly changing
science of biodiversity and community ecology.
Data analysis does not end with production
of statistical results. Those results have to be
interpreted in the light of other information about
the problem. We can not, therefore, discuss fully
the interpretation of the statistical results, or the
further statistical analyses they may lead to.
v
 Overview of methods described in
this manual
On the following page, a general diagram is
provided that describes the data analysis questions
that you can ask when analysing biodiversity
based on the methodologies that are provided in
this manual. Each question is discussed in further
detail in the respective chapter. The arrows
indicate the types of information that are used
in each method. All information is derived from
either the species data or the environmental data
of the sites. Chapter 2 describes the species and
environmental data matrices in greater detail.
Some methods only use information on species.
These methods are depicted on the left-hand side
of the diagram. They are based on biodiversity
statistics that can be used to compare the levels
of biodiversity between sites, or to analyse how
similar sites are in species composition.
The other methods use information on both
species and the environmental variables of the
sites. These methods are shown on the right-
hand side of the diagram. These methods provide
insight into the influence of environmental
vi
variables on biodiversity. The analysis methods
can reveal how much of the pattern in species
diversity can be explained by the influence of the
environmental variables. Knowing how much of
a pattern is explained will especially be useful if
the research was conducted to arrive at options
for better management of biodiversity. Note
that in this context, environmental variables
can include characteristics of the social and
economic environment, not only the biophysical
environment.
You may have noticed that Chapter 3 did
not feature in the diagram. The reason is that
this chapter describes how the Biodiversity.R
software can be installed and used to conduct
all the analyses described in the manual, whereas
you may choose to conduct the analysis with
different software. For this reason, the commands
and menu options for doing the analysis in
Biodiversity.R are separated from the descriptions
of the methods, and placed at the end of each
chapter.
vii
Effective data analysis requires familiarity with basic concepts and an Roeland Kindt is an ecologist
ability to use a set of standard tools, as well as creativity and imagination. with interests in community
Tree diversity analysis provides a solid practical foundation for training in ecology, conservation,
statistical methods for ecological and biodiversity studies. ecoagriculture and training.
He is currently leading a World
This manual arose from training researchers to analyse tree diversity data
Agroforestry Centre project on
collected on African farms, yet the statistical methods can be used for a
enhanced utilization of tree
wider range of organisms, for different hierarchical levels of biodiversity and
diversity at the landscape level.
for a variety of environments making it an invaluable tool for scientists and
students alike.
Richard Coe is a biometrician
Focusing on the analysis of species survey data, Tree diversity analysis and has more than 25 years
provides a comprehensive review of the methods that are most often used in experience in providing research
recent diversity and community ecology literature including: support to scientists in the elds
of ecology, agroforestry and
Species accumulation curves for site-based and individual-based species natural resource management.
accumulation, including a new technique for exact calculation of site- He is leading the Research
based species accumulation. Support Unit of the World
Agroforestry Centre.
Description of appropriate methods for investigating differences in
diversity and evenness such as Rnyi diversity proles, including methods
of rarefaction to the same sample size for different subsets of the data.

Modern regression methods of generalized linear models and generalized

additive models that are often appropriate for investigating patterns of
species occurrence and species counts.

Methods of ordination for investigating community structure and the

inuence of environmental characteristics, including recent methods
such as distance-based redundancy analysis and constrained analysis of
principal coordinates.

The manual also introduces a powerful new software programme,

Biodiversity.R, that is capable of performing all the statistical analyses
described in the book. The software is built using the free R language and
environment for statistical computing, and several of its libraries such as
the vegan community ecology package and the R-commander graphical
user interface. The software is provided on CD.

DFID
Department f o r
International
Development

World Agroforestry Centre, United Nations Avenue, Gigiri, PO Box 30677- 00100 Nairobi, Kenya
Tel: +254 20 7224000 Fax: +254 20 7224001 or via USA: Tel: +1 650 833 6645 Fax: +1 650 833 6646
Email: icraf@cgiar.org www.worldagroforestry.org


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